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| RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes T Brettin, JJ Davis, T Disz, RA Edwards, S Gerdes, GJ Olsen, R Olson, ... Scientific reports 5, 8365, 2015 | 531 | 2015 |
| Assemblathon 1: a competitive assessment of de novo short read assembly methods D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ... Genome research 21 (12), 2224-2241, 2011 | 496 | 2011 |
| Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center AR Wattam, JJ Davis, R Assaf, S Boisvert, T Brettin, C Bun, N Conrad, ... Nucleic acids research 45 (D1), D535-D542, 2016 | 347 | 2016 |
| Recovering complete and draft population genomes from metagenome datasets N Sangwan, F Xia, JA Gilbert Microbiome 4 (1), 8, 2016 | 119 | 2016 |
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| KBase: the United States department of energy systems biology knowledgebase AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ... Nature Biotechnology 36 (7), 2018 | 78 | 2018 |
| Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model K Tanaka, CS Henry, JF Zinner, E Jolivet, MP Cohoon, F Xia, V Bidnenko, ... Nucleic acids research 41 (1), 687-699, 2012 | 68 | 2012 |
| Antimicrobial resistance prediction in PATRIC and RAST JJ Davis, S Boisvert, T Brettin, RW Kenyon, C Mao, R Olson, R Overbeek, ... Scientific reports 6, 27930, 2016 | 67 | 2016 |
| Connecting genotype to phenotype in the era of high-throughput sequencing CS Henry, R Overbeek, F Xia, AA Best, E Glass, J Gilbert, P Larsen, ... Biochimica et Biophysica Acta (BBA)-General Subjects 1810 (10), 967-977, 2011 | 38 | 2011 |
| Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: unexpected abundance of clonal group 307 SW Long, RJ Olsen, TN Eagar, SB Beres, P Zhao, JJ Davis, T Brettin, ... MBio 8 (3), e00489-17, 2017 | 37 | 2017 |
| PATRIC as a unique resource for studying antimicrobial resistance DA Antonopoulos, R Assaf, RK Aziz, T Brettin, C Bun, N Conrad, JJ Davis, ... Briefings in bioinformatics, 2017 | 34 | 2017 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 34 | 2016 |
| Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models JP Faria, R Overbeek, F Xia, M Rocha, I Rocha, CS Henry Briefings in bioinformatics 15 (4), 592-611, 2013 | 34 | 2013 |
| Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes JJ Davis, F Xia, RA Overbeek, GJ Olsen International journal of systematic and evolutionary microbiology 63 (Pt 7 …, 2013 | 28 | 2013 |
| Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae M Nguyen, T Brettin, SW Long, JM Musser, RJ Olsen, R Olson, M Shukla, ... Scientific reports 8 (1), 421, 2018 | 26 | 2018 |
| Genome sequences of the primary endosymbiont “Candidatus Portiera aleyrodidarum” in the whitefly Bemisia tabaci B and Q biotypes ZF Jiang, F Xia, KW Johnson, E Bartom, JH Tuteja, R Stevens, ... Journal of bacteriology 194 (23), 6678-6679, 2012 | 25 | 2012 |
| Comparison of the genome sequences of “Candidatus Portiera aleyrodidarum” primary endosymbionts of the whitefly Bemisia tabaci B and Q biotypes ZF Jiang, F Xia, KW Johnson, CD Brown, E Bartom, JH Tuteja, R Stevens, ... Appl. Environ. Microbiol. 79 (5), 1757-1759, 2013 | 18 | 2013 |
| CANDLE/Supervisor: A workflow framework for machine learning applied to cancer research JM Wozniak, R Jain, P Balaprakash, J Ozik, NT Collier, J Bauer, F Xia, ... BMC bioinformatics 19 (18), 491, 2018 | 17 | 2018 |
